Contacts of the helix formed by residues 284 - 310 (chain A) in PDB entry 4LGD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 3.8 19.5 - - + -
128A LYS* 6.0 4.7 - - - -
129A SER* 5.1 9.9 - - - +
157A GLU 4.3 11.0 - - - +
158A GLY 3.6 19.7 - - - +
159A HIS* 4.0 31.0 - - + +
283A PRO* 1.3 72.5 - - + +
285A SER* 1.3 63.9 + - - +
286A ILE 3.1 0.7 - - - -
287A LEU* 3.1 21.2 + - - +
288A ARG 3.7 2.3 + - - -
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU 5.6 0.9 - - - -
283A PRO* 3.5 23.3 - - - +
284A VAL* 1.3 83.4 - - - +
286A ILE* 1.3 61.4 + - - +
287A LEU 3.1 0.2 - - - -
288A ARG* 2.9 36.0 + - - +
289A ASP* 4.2 3.8 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 3.0 45.1 - - + +
122A GLU* 3.8 11.5 - - + +
125A THR* 3.2 12.6 - - - +
282A LYS* 3.4 32.1 - - + +
283A PRO* 3.3 15.0 - - + +
285A SER* 1.3 83.0 - - - +
287A LEU* 1.3 66.6 + - + +
288A ARG 3.3 0.2 - - - -
289A ASP* 4.0 10.9 + - - +
290A LEU* 4.4 9.7 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 3.7 27.6 - - - +
125A THR* 3.5 27.1 - - + -
126A ILE* 3.8 14.4 - - + +
154A LEU* 4.2 13.7 - - + -
158A GLY 3.1 27.8 - - - +
160A ALA* 6.0 0.4 - - + -
284A VAL 3.1 10.4 + - - +
286A ILE* 1.3 74.3 - - + +
288A ARG* 1.3 57.4 + - - +
289A ASP 3.1 3.3 + - - -
290A LEU* 3.1 27.8 + - + +
291A ILE* 2.7 52.3 + - + +
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR 6.1 0.2 - - - -
157A GLU 5.0 8.5 + - - +
284A VAL 3.7 2.4 + - - +
285A SER* 2.9 28.5 + - - +
287A LEU* 1.3 79.5 - - - +
289A ASP* 1.3 62.8 + - - +
291A ILE* 3.7 8.8 - - - +
292A THR* 2.8 38.7 + - - +
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SER 4.2 3.0 + - - +
286A ILE 4.0 8.8 + - - +
287A LEU 3.1 0.6 - - - -
288A ARG* 1.3 86.3 - - - +
290A LEU* 1.3 64.7 + - - +
291A ILE 3.1 2.0 + - - -
292A THR* 3.4 6.4 + - - -
293A GLU* 3.3 34.2 + - - +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.9 25.6 - - + -
114A ARG* 3.1 36.8 - - - +
118A LEU* 4.8 5.6 - - + -
122A GLU* 3.3 44.6 - - + +
126A ILE* 5.3 2.5 - - + -
154A LEU* 4.7 6.3 - - + -
286A ILE 4.4 3.0 + - - +
287A LEU* 3.1 36.5 + - + +
289A ASP* 1.3 78.3 - - - +
291A ILE* 1.3 72.9 + - + +
293A GLU* 4.1 0.9 - - - -
294A ALA* 3.4 20.4 + - - +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 4.0 24.7 - - + -
110A ILE* 4.7 0.9 - - + -
154A LEU* 4.3 10.8 - - + -
155A ASN 4.2 3.6 - - - +
156A THR 4.0 12.6 - - - +
157A GLU 4.4 1.1 - - - -
158A GLY* 3.2 36.6 - - - +
287A LEU* 2.7 31.8 + - + +
288A ARG* 3.7 7.0 - - - +
290A LEU* 1.3 88.7 - - + +
292A THR* 1.3 60.3 + - - +
294A ALA* 3.4 5.1 + - - +
295A MET* 2.9 49.7 + - + +
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 2.8 27.2 + - - +
289A ASP* 3.4 7.1 + - - -
291A ILE* 1.3 76.3 - - - +
293A GLU* 1.3 56.4 + - + +
295A MET* 3.9 14.3 - - + +
296A GLU* 2.7 47.0 + - + +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.1 37.1 + - + -
116A LYS* 4.4 12.2 + - - +
289A ASP* 3.3 20.9 + - - +
290A LEU 4.1 0.4 - - - +
291A ILE 3.3 0.2 - - - -
292A THR* 1.3 79.1 - - + +
294A ALA* 1.3 56.4 + - - +
296A GLU* 3.3 11.6 + - - +
297A ILE* 2.9 43.2 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 5.0 3.1 - - + +
110A ILE* 3.9 31.6 - - + -
113A LEU* 3.8 19.5 - - + +
114A ARG* 4.1 11.8 - - + +
290A LEU 3.4 15.9 + - - +
291A ILE* 3.4 5.8 + - - +
292A THR 3.3 0.6 - - - -
293A GLU* 1.3 79.6 - - - +
295A MET* 1.3 58.4 + - + +
297A ILE* 3.4 5.2 + - - +
298A LYS* 2.9 28.1 + - - +
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY 4.4 6.1 - - - +
104A ALA* 4.1 23.1 - - - -
156A THR* 4.0 35.9 - - + +
291A ILE* 2.9 39.4 + - + +
292A THR* 4.0 12.1 - - + +
294A ALA* 1.3 73.8 - - + +
296A GLU* 1.3 60.7 + - - +
298A LYS* 3.2 13.0 - - + +
299A ALA* 3.0 27.2 + - - +
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 2.7 31.2 + - + +
293A GLU* 3.6 11.1 - - - +
295A MET* 1.3 70.9 - - - +
297A ILE* 1.3 62.7 + - - +
299A ALA* 2.9 9.8 + - + +
300A LYS* 2.8 40.4 + - + +
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 4.2 19.7 - - + +
114A ARG* 4.1 28.9 - - + +
293A GLU* 2.9 29.5 + - + +
294A ALA* 3.7 4.3 - - - +
296A GLU* 1.3 78.6 - - + +
298A LYS* 1.3 58.1 + - - +
300A LYS* 3.7 21.3 - - + +
301A ARG* 2.9 45.6 + - + +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 5.9 3.8 - - - +
33A LEU* 4.7 31.1 + - + +
103A GLY 3.6 23.7 + - - +
104A ALA 4.5 2.7 + - - +
105A GLY* 4.2 16.2 - - - +
109A ASP* 5.7 4.0 + - - +
113A LEU* 4.3 28.3 - - + +
294A ALA 2.9 13.0 + - - +
295A MET* 3.2 18.8 - - + +
296A GLU 3.1 0.4 - - - -
297A ILE* 1.3 78.7 - - - +
299A ALA* 1.3 52.6 + - - +
301A ARG* 4.0 10.4 - - - +
302A HIS* 3.2 24.4 + - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A MET 3.0 11.3 + - - +
296A GLU* 2.9 12.6 + - + +
298A LYS* 1.3 75.4 - - - +
300A LYS* 1.3 64.9 + - - +
301A ARG 3.2 0.2 - - - -
302A HIS* 3.0 7.8 + - - +
303A GLU* 2.9 29.4 + - - +
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU* 2.8 30.9 + - + +
297A ILE* 3.7 23.0 - - + +
299A ALA* 1.3 72.8 - - - +
301A ARG* 1.3 57.8 + - + +
303A GLU* 3.3 18.6 - - - +
304A GLU* 2.9 44.2 + - + +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 3.7 21.0 - - - +
113A LEU* 3.6 27.8 - - - +
297A ILE* 2.9 31.3 + - + +
298A LYS* 4.0 12.1 + - - +
300A LYS* 1.3 74.6 - - + +
302A HIS* 1.3 61.3 + - - +
304A GLU* 3.9 10.7 - - - +
305A GLN* 2.8 41.2 + - - +
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Residues in contact with HIS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.3 45.8 + - + +
32A LYS 4.9 5.8 + - - -
298A LYS 3.2 14.0 + - - +
299A ALA* 3.0 12.7 + - - +
301A ARG* 1.3 80.5 - - - +
303A GLU* 1.3 60.4 + - - +
305A GLN* 3.8 4.0 - - - +
306A GLN* 2.9 52.0 + - + +
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 2.9 15.4 + - - +
300A LYS* 3.3 25.9 - - - +
302A HIS* 1.3 78.4 + - - +
304A GLU* 1.3 70.3 + - + +
306A GLN* 3.9 6.3 - - - +
307A ARG* 3.1 26.2 + - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LYS* 2.9 33.6 + - + +
301A ARG* 3.9 12.3 - - - +
303A GLU* 1.3 79.6 - - + +
305A GLN* 1.3 58.5 + - - +
307A ARG* 3.9 5.7 + - - +
308A GLU* 3.2 43.5 + - - +
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Residues in contact with GLN 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 2.8 25.0 + - - +
302A HIS* 3.9 4.0 - - - +
304A GLU* 1.3 76.9 - - - +
306A GLN* 1.3 58.4 + - - +
307A ARG 3.2 1.8 - - - -
308A GLU* 3.3 15.2 + - + +
309A LEU* 3.1 37.3 + - + +
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A HIS* 2.9 43.2 + - + +
303A GLU* 3.3 6.9 + - - +
305A GLN* 1.3 77.8 - - - +
307A ARG* 1.3 60.8 + - - +
309A LEU* 3.4 24.2 - - + +
310A GLU* 3.3 28.1 + - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU 3.1 16.2 + - - +
304A GLU* 4.1 6.7 - - - +
306A GLN* 1.3 75.4 - - - +
308A GLU* 1.3 61.5 + - + +
310A GLU* 4.0 9.5 - - - +
311A GLU* 2.9 56.3 + - + +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.2 35.9 - - + +
305A GLN* 3.3 17.1 + - + +
306A GLN 3.2 0.6 - - - -
307A ARG* 1.3 78.2 - - + +
309A LEU* 1.3 60.9 + - - +
310A GLU 3.1 5.2 + - - -
311A GLU* 3.3 16.7 + - - +
312A GLU* 3.5 17.5 + - - +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLN* 3.1 29.7 + - + +
306A GLN* 3.4 25.4 - - + +
308A GLU* 1.3 76.0 - - - +
310A GLU* 1.3 67.4 + - + +
311A GLU 3.4 0.2 - - - -
312A GLU 5.0 0.7 - - - -
313A GLU* 4.1 18.8 + - - +
451A ARG* 6.2 2.2 - - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN* 3.3 25.0 + - + +
307A ARG* 4.2 9.7 - - - +
308A GLU 3.1 0.8 - - - -
309A LEU* 1.3 86.1 - - + +
311A GLU* 1.3 62.1 + - + +
313A GLU* 3.7 21.3 - - - +
447A GLU* 4.1 20.0 - - - +
451A ARG* 5.2 14.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il